Manchester City midfielder Foden followed up a rebound to give England a half-time lead and lashed home his second in stoppage time.
The Young Lions followed up Friday's 3-2 victory in Turkey by ensuring six points from their opening two Group Three matches.
Aidy Boothroyd's side should have won by a bigger margin and it was for long periods a frustrating night for a crowd of 15,258 as the hosts failed to cash in on their dominance.
Kosovo, top of Group Three at kick-off after wins against Andorra and Turkey, began full of confidence and forced England goalkeeper Aaron Ramsdale into the first save.
Winger Lirim Kastrati, not to be confused with Kosovo's left-back who has the same name, raced on to a ball over the top and saw his low shot turned away for a corner.
England made just one change from the side that won in Turkey, with Norwich defender Ben Godfrey in for Jonathan Panzo, but were slow into their stride.
They had only just begun to find any kind of cohesion by the time Foden gave them a 25th-minute lead.
Steven Sessegnon's shot was cleared off the goal-line by defender Kastrati and Foden followed up to force the ball home.
Foden's influence grew and so did England's dominance. Tom Davies headed Foden's corner narrowly over and Reiss Nelson's shot from inside the area was well saved by Kosovo goalkeeper Florjan Smakiqi.
Kosovo served warning of their threat on the break just before half-time when Ardit Gashi lashed a low effort narrowly wide.
England should have doubled their lead soon after the restart, but Eddie Nketiah pulled his low effort wide.
Todd Cantwell and Mason Greenwood replaced Reiss Nelson and Morgan Gibbs-White just after the hour-mark as England looked to turn their superiority into more goals.
Cantwell's shot was fumbled for a corner by Smakiqi, but they still had little to show for all their possession and only a brave lunge in the box by Max Aarons denied Kosovo a clear scoring chance.
Aarons limped off and was replaced by James Justin and as England looked set to settle for a single-goal win, Foden pounced on a loose ball in the area in the fourth minute of added time and lashed his shot into the top corner.